Citing

Citing your use of PDB2PQR

Please acknowledge your use of PDB2PQR by citing:

  • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. (Link)
  • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. (Link)

Please acknowledge your use of PEOE_PB protein/ligand parameterization software by citing:

  • Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins, 65, 424-437, 2006. (Link)

Citing your use of APBS

Please acknowledge your use of APBS by citing:

  • Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. (Link) Additional articles discussing APBS and the PBE are available from the [suggested reading]

Please acknowledge your use of the Holst group software by citing:

  • M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
  • M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995. for PMG (the multigrid solver) or
  • M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001 (Link).
  • R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. (Link) for FEtk (the finite element solver).